In December 2000, the Equal Employment Opportunity Commission ruled that companies that provided prescription drugs to their employees but didn't provide birth control were in violation of Title VII of the 1964 Civil Rights Act, which prevents discrimination on the basis of sex. That opinion, which the George W. Bush administration did nothing to alter or withdraw when it took office the next month, is still in effect today—and because it relies on Title VII of the Civil Rights Act, it applies to all employers with 15 or more employees. Employers that don't offer prescription coverage or don't offer insurance at all are exempt, because they treat men and women equally—but under the EEOC's interpretation of the law, you can't offer other preventative care coverage without offering birth control coverage, too.
Not even religious employers were exempt from the impact of the EEOC decision. Although Title VII allows religious institutions to discriminate on religious grounds, it doesn't allow them to discriminate on the basis of sex—the kind of discrimination at issue in the EEOC ruling. DePaul University, the largest Roman Catholic university in America, added birth control coverage to its plans after receiving an EEOC complaint several years ago.
The current additions to the policy are that there is to be no copay for BC coming from insurance companies and that employers who employ under 15 people are no longer exempt.
http://www.eeoc.gov/policy/docs/decision-contraception.html
http://biotech.law.lsu.edu/cases/eeoc/Erickson_v_Bartell.htm
http://www.civilrights.org/lgbt/enda/religious-exemption-1.html
If churches feel that this is unfair than they actually have the choice to simply drop prescription coverage to remain in compliance with EEOC. We all know that health care isn't a constitutional right, right?